Contacts of the helix formed by residues 51 - 71 (chain K) in PDB entry 5A0Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 51 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K ALA* 1.3 78.4 - - - +
52K ASP* 1.3 54.6 + - - +
53K THR 3.2 0.4 - - - -
54K VAL* 3.0 6.4 + - - -
55K GLN* 2.4 51.9 + - - +
88L TYR* 5.1 2.5 - - - -
91L LYS* 4.8 0.2 - - - +
117L GLU 3.4 16.2 + - - -
118L GLY* 4.2 16.0 - - - -
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Residues in contact with ASP 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLU 4.0 12.3 - - - +
50K ALA* 3.2 1.4 - - - +
51K GLY* 1.3 76.3 - - - +
53K THR* 1.3 56.6 + - - +
55K GLN* 4.2 2.0 - - - -
56K PHE* 3.0 32.6 + - - +
96K THR* 4.6 2.1 + - - -
97K PRO 4.5 2.6 - - - +
98K TYR* 3.1 31.5 - - + -
99K HIS* 4.2 8.0 + - + +
100K VAL* 3.6 13.1 - - + +
88L TYR* 1.9 45.5 + - - -
91L LYS* 5.0 10.5 + - - +
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Residues in contact with THR 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K HIS* 5.6 2.6 + - - -
36K PHE* 4.1 4.5 - - - -
46K CYS* 3.9 30.3 + - - +
47K VAL 4.3 0.9 - - - +
48K GLY* 2.8 48.7 - - - +
49K GLU 3.7 3.4 - - - +
50K ALA 3.4 12.6 + - - +
52K ASP* 1.3 76.6 - - - +
54K VAL* 1.3 73.7 + - - +
56K PHE* 4.2 0.7 - - - +
57K ALA* 3.1 24.6 + - - +
99K HIS 4.6 2.5 - - - +
100K VAL* 3.9 8.7 - - - -
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Residues in contact with VAL 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K HIS* 5.4 11.4 - - + +
36K PHE* 3.8 27.8 - - + -
50K ALA 4.8 3.4 - - - +
51K GLY* 3.0 7.1 + - - +
53K THR* 1.3 89.0 + - - +
55K GLN* 1.3 65.5 + - - +
56K PHE 3.1 1.6 - - - -
57K ALA* 4.0 2.7 - - + +
58K GLU* 3.1 53.6 + - + +
81L LYS* 5.2 4.7 - - - +
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Residues in contact with GLN 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 5.5 6.0 - - - +
51K GLY* 2.4 42.4 + - - +
52K ASP* 4.2 1.8 - - - -
54K VAL* 1.3 67.8 - - - +
56K PHE* 1.3 56.0 + - - +
58K GLU* 5.1 1.0 - - - +
59K TYR* 3.3 21.3 + - - +
98K TYR* 5.2 6.4 + - + +
81L LYS* 3.8 11.4 + - - +
84L ALA* 4.9 1.7 - - - +
85L ASN* 3.5 28.8 + - - +
88L TYR* 2.7 56.0 - - + +
118L GLY* 6.4 0.2 - - - -
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Residues in contact with PHE 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K LEU* 3.8 17.9 - - + -
52K ASP 3.0 21.6 + - - +
53K THR 4.2 3.4 - - - +
55K GLN* 1.3 78.5 - - - +
57K ALA* 1.3 70.9 + - + +
58K GLU 3.3 0.4 - - - -
59K TYR* 3.0 22.5 + + - +
60K ILE* 3.0 40.0 + - + +
84K THR* 2.7 29.8 - - - -
87K ASN* 4.1 9.9 - - + -
88K LEU* 3.2 37.0 - - + -
98K TYR* 4.1 21.3 - + + -
100K VAL* 4.5 15.0 - - + -
102K LEU* 4.6 6.7 - - + -
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Residues in contact with ALA 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K PHE* 3.8 34.1 - - + -
38K MET* 3.2 20.0 - - + +
44K LEU* 4.7 3.1 - - + -
46K CYS* 5.2 0.9 - - + -
53K THR 3.1 20.4 + - - +
54K VAL* 3.3 5.3 + - + -
56K PHE* 1.3 91.0 - - + +
58K GLU* 1.3 58.7 + - + +
60K ILE* 3.2 2.6 + - - +
61K GLN* 2.9 22.1 + - - +
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Residues in contact with GLU 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ARG 6.0 0.2 - - - -
96D LEU* 3.7 25.4 - - + +
36K PHE* 6.0 1.1 - - + -
54K VAL* 3.1 33.3 + - + +
55K GLN* 5.1 0.7 - - - +
57K ALA* 1.3 77.3 - - + +
59K TYR* 1.4 54.8 + - - +
61K GLN* 2.9 14.3 + - - +
62K LYS* 2.9 49.4 + - - +
81L LYS* 3.2 36.1 + - - +
120L ARG* 5.2 5.2 + - - -
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Residues in contact with TYR 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 3.9 12.2 - - + +
55K GLN 3.3 20.7 + - - +
56K PHE* 3.0 16.1 + + - +
58K GLU* 1.4 76.1 - - - +
60K ILE* 1.3 63.3 + - + +
62K LYS* 4.7 2.3 - - - +
63K ASN* 2.8 46.6 + - - -
87K ASN* 3.3 35.9 + - + -
98K TYR* 5.2 11.4 - + - -
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Residues in contact with ILE 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K MET* 4.1 11.2 - - - -
44K LEU* 4.8 8.5 - - + -
56K PHE* 3.0 45.6 + - + +
57K ALA 3.4 6.7 - - - +
59K TYR* 1.3 83.4 - - + +
61K GLN* 1.3 63.2 + - - +
63K ASN* 3.0 5.4 + - - +
64K VAL* 3.0 37.2 + - + +
80K ALA* 5.2 2.0 - - + +
83K PHE* 4.1 15.0 - - + -
84K THR* 4.2 12.1 - - - +
87K ASN* 3.0 37.0 - - - +
104K LEU* 6.0 0.4 - - + -
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Residues in contact with GLN 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ARG* 6.3 0.6 - - - +
36K PHE* 5.5 2.3 - - - +
37K LYS 3.4 23.5 + - - +
38K MET* 3.5 42.8 + - + +
57K ALA 2.9 7.7 + - - +
58K GLU* 2.9 18.7 + - - +
60K ILE* 1.3 75.9 - - - +
62K LYS* 1.3 77.5 + - + +
64K VAL* 3.2 3.6 + - - +
65K GLN* 2.9 38.2 + - + +
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Residues in contact with LYS 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLN* 3.4 48.6 + - + +
93D SER* 6.0 0.2 - - - -
95D ARG* 3.9 23.8 + - + +
96D LEU* 3.8 35.6 - - + +
58K GLU* 2.9 44.5 + - - +
59K TYR* 4.7 3.8 - - - +
60K ILE 3.3 0.2 - - - -
61K GLN* 1.3 99.0 + - + +
63K ASN* 1.4 57.9 + - - +
65K GLN* 5.5 0.4 - - + -
66K LEU* 2.9 27.2 + - - +
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Residues in contact with ASN 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 4.9 5.2 + - - +
59K TYR* 2.8 43.6 + - - -
60K ILE 3.0 8.0 + - - +
62K LYS* 1.4 75.9 - - - +
64K VAL* 1.3 58.4 + - - +
66K LEU* 3.0 18.0 + - - +
67K TYR* 2.9 32.6 + - - +
83K PHE* 3.6 31.3 - - + -
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Residues in contact with VAL 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 5.5 0.4 - - - -
38K MET* 4.2 17.3 - - + +
39K SER* 3.6 23.5 + - - +
42K ILE* 4.6 15.3 - - + -
60K ILE* 3.0 34.7 + - + +
61K GLN* 3.2 5.8 + - - +
63K ASN* 1.3 74.9 - - - +
65K GLN* 1.3 60.6 + - - +
67K TYR* 3.6 13.0 - - - +
68K LYS* 3.6 8.1 + - - +
75K LEU* 4.0 21.5 + - + +
80K ALA* 4.7 12.6 - - + -
83K PHE* 4.0 16.6 - - + -
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Residues in contact with GLN 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLN* 3.5 22.6 + - - +
95D ARG* 6.6 0.4 - - - -
38K MET 3.0 25.6 - - - +
39K SER* 3.6 13.3 + - - -
61K GLN* 2.9 26.8 + - + +
62K LYS* 5.2 0.9 - - + -
64K VAL* 1.3 74.8 - - - +
66K LEU* 1.3 62.9 + - - +
67K TYR 3.2 2.0 - - - -
68K LYS* 3.1 35.0 + - - +
69K MET* 3.3 30.1 + - + +
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Residues in contact with LEU 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ARG* 3.6 34.5 - - + +
89D VAL* 4.0 14.6 - - + +
92D GLN* 3.9 13.9 - - + +
62K LYS 2.9 20.5 + - - +
63K ASN* 3.0 20.4 + - - +
65K GLN* 1.3 75.1 - - - +
67K TYR* 1.4 56.2 + - - +
69K MET* 3.4 5.8 + - + +
70K ARG* 3.1 65.6 + - + +
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Residues in contact with TYR 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TYR* 2.8 37.1 + + - -
101C TYR* 4.2 15.7 - + - +
103C GLU* 3.5 5.5 + - - -
106C PRO* 4.8 0.2 - - - +
109C GLN* 3.6 9.5 + - - -
142C HIS* 4.7 3.3 + - - -
63K ASN 2.9 15.5 + - - +
64K VAL 3.6 6.5 - - - +
66K LEU* 1.4 74.5 - - - +
68K LYS* 1.3 57.3 + - - +
70K ARG* 4.3 5.6 - - - +
71K ASN* 2.8 60.4 + - - +
73K TYR* 3.5 35.0 - + - -
75K LEU* 3.0 54.3 - - + +
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Residues in contact with LYS 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K SER* 5.9 1.1 - - - +
40K GLU* 5.9 0.8 + - - -
64K VAL 3.6 9.7 + - - +
65K GLN* 3.1 32.7 + - - +
67K TYR* 1.3 80.0 - - - +
69K MET* 1.3 63.0 + - + +
72K GLY* 3.0 25.1 + - - -
73K TYR* 3.5 22.8 - - - +
74K GLU* 4.3 32.1 + - + +
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Residues in contact with MET 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 4.1 19.9 - - - +
65D LEU 4.1 10.5 - - - +
66D ASP* 3.8 34.1 - - - +
67D ASP* 4.1 6.7 - - + +
88D ARG* 3.0 40.7 + - + +
92D GLN* 5.0 10.8 - - + +
95D ARG* 5.6 2.9 - - - +
65K GLN* 3.3 26.2 + - + +
66K LEU* 3.9 7.6 - - + +
67K TYR 3.2 0.6 - - - -
68K LYS* 1.3 84.9 - - + +
70K ARG* 1.3 62.9 + - - +
71K ASN 3.3 0.6 + - - -
72K GLY* 4.1 4.6 + - - -
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Residues in contact with ARG 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLU* 5.7 0.9 - - - +
112C THR* 6.1 0.7 - - - +
116C ASP* 5.5 3.2 + - - -
85D ASN* 3.3 57.1 + - - +
88D ARG* 3.8 19.1 + - - +
89D VAL* 3.4 20.6 - - - +
66K LEU* 3.1 40.6 + - - +
67K TYR* 3.1 7.8 + - - +
69K MET* 1.3 76.7 - - - +
71K ASN* 1.3 72.0 + - - +
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Residues in contact with ASN 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLU* 5.3 7.2 - - - +
109C GLN* 3.4 37.8 - - + +
112C THR* 5.7 0.9 + - - -
143C TYR* 4.9 1.0 + - - -
67K TYR* 2.8 58.5 + - + +
70K ARG* 1.3 96.5 - - - +
72K GLY* 1.3 56.0 + - - +
73K TYR* 3.1 33.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il